Question: (Closed) Is there any specially designed software or a web service for the VCF file similarity search?
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gravatar for genome21
2.4 years ago by
genome2110
genome2110 wrote:

Is there any specially designed software or a web service for the VCF file similarity search, producing a report? Is there anything good beyond VCF compare commands in VCF, BCF tools, GATK?

vcf • 561 views
ADD COMMENTlink written 2.4 years ago by genome2110

This question doesn't contain enough information. Please specify which input you have (and how many samples) and which would be the desired output.

ADD REPLYlink written 2.4 years ago by WouterDeCoster40k

Is there anything good beyond VCF compare commands in VCF, BCF tools, GATK?

what's wrong/missing with those tools ?

ADD REPLYlink written 2.4 years ago by Pierre Lindenbaum121k

Hello genome21!

We believe that this post does not fit the main topic of this site.

Not a real question

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.4 years ago by Michael Dondrup46k

It depends on the reason you want to compare VCF files. What is the measure of similarity for you? In population analysis ADMIXTURE https://www.genetics.ucla.edu/software/admixture/ is one of the ways to cluster and then transform vcf files to vectors (called admixture vectors) and then compare these vectors. By admixture design vectors from within the same population will be closer.

If you want to find relatedness between two VCF samples you can look at the IBD with plink or use dedicated programs like KING to find kinship http://people.virginia.edu/~wc9c/KING/manual.html

Could you please specify your question?

ADD REPLYlink written 2.4 years ago by Petr Ponomarenko2.6k
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